Main
Dr. Alexander Shakeel Bates
I am a neuroscientist and programmer on open-source projects. I work on insect brains. I am interested in how neurons wire together, and how they work together to build complex, innate behaviours. D.O.B. 23/09/1993.
| total_cites | h_index | i10_index |
|---|---|---|
| 1990 | 17 | 17 |
Professional Research
Postdoctoral Fellow in Neurobiology
Harvard Medical School
Boston, US
present - 01/10/2020
- Member of the laboratory of Prof. Rachel Wilson
- Working on navigational circuitry, using calcium imaging, neurophysiology and behavioural studies involving virtual reality with D. melanogaster
Visiting Scientist
Dept. Zoology, University of Cambridge
remote
present - 01/10/2020
- Neuroinformatics work with the Drosophila Connectomics Group
- Developed R tools for neuroanatomy and connectomics
Grants
Sir Henry Wellcome Fellowship
Wellcome Trust & University of Oxford
UK
01/06/2025 - 01/06/2022
- 30,000 GBP towards my current research
- Collaboration between groups of Rachel Wilson, Wei Lee, Scott Waddell and Shaul Druckmann
Human Frontiers Fellowship
International Human Frontier Science Program
International
2021
- Did not pursue
Boehringer Ingelheim PhD Scholarship
Boehringer Ingelheim Foundation
European
01/08/2018 - 01/08/2016
Skills
- R
- python
- MATLAB
- github
- git
- markdown
- Illustrator
- InDesign
- communication
- text editing
- journalistic writing
- creative writing
- open access
Peer Reviews
| journal | reviews |
|---|---|
| PLoS Computational Biology | 3 |
| eLife | 3 |
| Nature Communications | 1 |
Referees
PhD Supervisor: Dr. Gregory Jefferis, MRC Laboratory of Molecular Biology, Cambridge, jefferis@mrc-lmb.cam.ac.uk
Current Supervisor: Prof. Rachel Wilson, Harvard Medical School, Rachel_Wilson@ hms.harvard.edu
BSc Tutor at UCL: Dr. Marco Beato, UCL Neuroscience, Physiology and Pharmacology, m.beato@ucl.ac.uk
Supervisee: Serene Dhawan, Princeton, PhD student, serenedhawan @gmail.com
Education
Neuroscience PhD
MRC LMB, University of Cambridge
Cambridge, UK
30/09/2020 - 01/09/2015
- PhD student with Dr. Greg Jefferis
- Thesis: The lateral horn, a brain region in the fly, primes innate olfactory behaviours by combining patterns of second-order olfactory projection neuron activity. In my work, I developed tools and analyses, and reconstructed neural networks from electron microscopy data, in order to better understand this brain region and how memory systems interact with it
- Neuroinformatics, data science, R programming
- Awards: Honorary Vice Chancellor’s Award, MRC LMB Max Perutz Prize 2019, Winner of the British Neuroscience Association Postgraduate Prize 2020
Neuroscience BSc
University College London
London, UK
01/07/2015 - 01/09/2012
- 1st class degree with honours
- Modules taken listed on linkedIn
- Awards: Burnstock Sessional Prize in Neuroscience BSc (ranked first in year) (2012–2013) (2013-2014) (2014-2015), Dean’s list for the Faculty of Life Sciences (2013-2014) (2014-2015), Rob Clarke Award from the Society of Physiology
A levels
Woodbridge High School
London, UK
01/09/2012 - 01/09/2010
- 6 A*s at A-level, comprising: Physics, Chemistry, Mathematics, English Literature, Philosophy and Russian, and in a history related EPQ (level 3) project
GCSEs
Woodbridge High School
London, UK
31/08/2010 - 01/09/2008
- 13 A*s: English Literature, English Language, Mathematics, Statistics, Core Science, Additional Science, History, Philosophy, Geography, French, Italian, Russian and Expressive Arts. Jack Petchey Achievement Award
Reviews
| title | author | journal | year | cites | |
|---|---|---|---|---|---|
| 1 | Systems neuroscience: Auditory processing at synaptic resolution | AS Bates, G Jefferis | Current Biology | 2022 | 1 |
| 6 | Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics | AS Bates, J Janssens, GS Jefferis, S Aerts | Current opinion in neurobiology | 2019 | 59 |
Papers
This table shows all of my work, searchable on pubmed. Author list displays firt six. My name in bold, underlining indicates first (co)authorship. Get in contact for information on recents projects.
Most of my work has first been published on bioRxiv
Much of my work comes with open source R code
| title | author | journal | year | cites | |
|---|---|---|---|---|---|
| 2 | Information flow, cell types and stereotypy in a full olfactory connectome | P Schlegel, AS Bates, T Stürner, SR Jagannathan, N Drummond, J Hsu, … | Elife | 2021 | 89 |
| 3 | Complete connectomic reconstruction of olfactory projection neurons in the fly brain | AS Bates, P Schlegel, RJV Roberts, N Drummond, IFM Tamimi, … | Current Biology | 2020 | 140 |
| 4 | Neurotransmitter Classification from Electron Microscopy Images at Synaptic Sites in Drosophila Melanogaster | N Eckstein, AS Bates, A Champion, M Du, Y Yin, P Schlegel, AKY Lu, … | bioRxiv | 2020 | 65 |
| 5 | The natverse, a versatile toolbox for combining and analysing neuroanatomical data | AS Bates, JD Manton, SR Jagannathan, M Costa, P Schlegel, T Rohlfing, … | Elife | 2020 | 135 |
| 7 | Functional and anatomical specificity in a higher olfactory centre | S Frechter, AS Bates, S Tootoonian, MJ Dolan, J Manton, AR Jamasb, … | Elife | 2019 | 84 |
| 8 | Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila | P Schlegel, Y Yin, AS Bates, S Dorkenwald, K Eichler, P Brooks, DS Han, … | bioRxiv | 2023 | 19 |
| 9 | Discriminative attribution from paired images | N Eckstein, H Bukhari, AS Bates, GSXE Jefferis, J Funke | European Conference on Computer Vision | 2022 | 4 |
| 10 | BAcTrace, a tool for retrograde tracing of neuronal circuits in Drosophila | S Cachero, M Gkantia, AS Bates, S Frechter, L Blackie, A McCarthy, … | Nature methods | 2020 | 25 |
| 11 | Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body | MJ Dolan, S Frechter, AS Bates, C Dan, P Huoviala, RJ Roberts, … | Elife | 2019 | 124 |
| 12 | Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila | MJ Dolan, G Belliart-Guérin, AS Bates, S Frechter, A Lampin-Saint-Amaux, … | Neuron | 2018 | 93 |
| 13 | Automated reconstruction of a serial-section EM Drosophila brain with flood-filling networks and local realignment | PH Li, LF Lindsey, M Januszewski, Z Zheng, AS Bates, I Taisz, M Tyka, … | bioRxiv | 2019 | 85 |
| 14 | Network Statistics of the Whole-Brain Connectome of Drosophila | A Lin, R Yang, S Dorkenwald, A Matsliah, AR Sterling, P Schlegel, S Yu, … | bioRxiv | 2023 | 0 |
| 15 | Neuronal wiring diagram of an adult brain | S Dorkenwald, A Matsliah, AR Sterling, P Schlegel, SC Yu, CE McKellar, … | bioRxiv | 2023 | 26 |
| 16 | A leaky integrate-and-fire computational model based on the connectome of the entire adult Drosophila brain reveals insights into sensorimotor processing | PK Shiu, GR Sterne, N Spiller, R Franconville, A Sandoval, J Zhou, … | bioRxiv | 2023 | 4 |
| 17 | The connectome of the adult Drosophila mushroom body provides insights into function | F Li, JW Lindsey, EC Marin, N Otto, M Dreher, G Dempsey, I Stark, … | Elife | 2020 | 221 |
| 18 | A connectome and analysis of the adult Drosophila central brain | LK Scheffer, CS Xu, M Januszewski, Z Lu, S Takemura, KJ Hayworth, … | Elife | 2020 | 648 |
| 19 | Connectomics analysis reveals first-, second-, and third-order thermosensory and hygrosensory neurons in the adult Drosophila brain | EC Marin, L Büld, M Theiss, T Sarkissian, RJV Roberts, R Turnbull, … | Current Biology | 2020 | 75 |
| 20 | Input connectivity reveals additional heterogeneity of dopaminergic reinforcement in Drosophila | N Otto, MW Pleijzier, IC Morgan, AJ Edmondson-Stait, KJ Heinz, I Stark, … | Current Biology | 2020 | 50 |
| 21 | Neural circuit basis of aversive odour processing in Drosophila from sensory input to descending output | P Huoviala, MJ Dolan, FM Love, P Myers, S Frechter, S Namiki, … | bioRxiv | 2018 | 40 |
| 22 | Combinatorial encoding of odors in the mosquito antennal lobe | P Singh, S Goyal, S Gupta, S Garg, A Tiwari, V Rajput, AS Bates, … | Nature Communications | 2023 | 3 |
Selected Talks
ECRO meeting
European Chemoreception Research Organization
Trieste, Italy
2019
Boehringer Ingelheim Meeting
Boehringer Ingelheim Fonds
Hirschegg, Austria
2018
MPI Connectomics meeting
Max Planck Institute
Berlin, Germany
2017
ECRO meeting
European Chemoreception Research Organization
Cambridge, UK
2017
Boehringer Ingelheim Meeting
Boehringer Ingelheim Fonds
Hirschegg, Austria
2017
Brains and Roses
Schaeffer and Datta group organised
Montserrat, Catalonia
2016
Selected Posters
HHMI Investigators’ Meeting
HHMI HQ
Chevy Chase
2023
UK Neural Computation
University of Nottingham
Nottingham, UK
2019
Boehringer Ingelheim Fonds communication workshop
Boehringer Ingelheim Foundation
Mainz, Germany
2017
Maggot Meeting
Janelia Research Campus
Ashburn, US
2016
High-resolution circuit reconstruction meeting
Janelia Research Campus
Ashburn, US
2016
LMB GSA Symposium
MRC LMB, University of Cambridge
Cambridge, UK
2016
Leadership
Mentored summer student
MRC LMB, University of Cambridge
Cambridge, UK
2018
Mentored undergraduate student
Dept. Zoology, University of Cambridge
Cambridge, UK
01/05/2018 - 01/09/2017
- Student won best thesis in year award and two authorships
Mentored summer student
MRC LMB, University of Cambridge
Cambridge, UK
2017
UCL iGEM 2014 Advisor
University College London
London, UK
2014
- Project planning, oversight, team slection and management
- Gold medallist
Other
Visiting Scholar
Janelia Research Campus
Ashburn, US
2019
- Worked in FlyEM, Dr. Gerry Rubin’s Group
- Worked on the hemibrain connectome
Paris Spring School in Neuroscience Techniques
Paris Descartes University
Paris, France
2018
- A course in Optical Imaging and Electrophysiological Recording in Neuroscience
Visiting Scholar
Janelia Research Campus
Ashburn, US
2016
- Worked with Dr. Albert Cardona’s Group
- Worked on the L1 larval connectome
University of Queensland Winter Scholarship
University of Queensland
Brisbane, Australia
2015
- Worked on tectal activity in zebrafish larvae, light sheet imaging, Dr. Ethan Scott’s Group
Amgen Scholarship
Dept. Zoology, University of Cambridge
Cambridge, UK
2014
- Worked on neuronal structural plasticity in D. melanogaster larvae, Dr. Landgraf’s group
UCL iGEM 2013 team member
University College London
London, UK
2013
- Team member, cloning, cell culture, project planning
- Gold medallist
Summer student in the biomolecular modelling laboratory
Cancer Research UK, London Research Institute
London, UK
2013
- Student Placement with Dr. Tammy Cheng, python programming
Disclaimer
Made with the R package pagedown and datadrivencv.
Code available on GitHub.
Last updated on 2023-11-27.